A fly cutter is used on a milling machine , it is a single point cutter, and produces a fine or coarse finish depending on feed rate.
No fly cutter, then 100 grit will give a suitably ruff finish. if you lap on a flat surface be sure to use a figure of eight pattern ,if not it will end up curved not flat.This should be done in a Zen like manner, slow and calm.
its worth seeking out a friendly mill operator, not just for flattening , its the best way to spot face the fastener seats.
Yup re torquing is a PITA , sometimes I mark with paint, slacken then retorque , noting any movement. other times I have just gone over and nipped up to torque, on my bike usually the centre bolt takes a bit more, no way to get at the front two without moving the ex rocker spindle and push rods. Its a one time deal and well worth the bother IMO.
Most important is to sneak up on the torgue 5 fitpunds at a time on initial fitting.
One more important thing, do not assume the barrel top surface is dead flat,it often isnt. It can be lapped in the same way as the head. .
Barrel to head interface can be checked by bluing the head and shimmy ing against the barrel, sometimes its just one or two high spots around the fastener heads, these can be locally scraped.